I have a vague memory that this issue was addressed by MSR in the 70s when they first developed the stove. I think the very first models couldn't tolerate constant immersion in the fuel. Subsequent models were designed with materials that could tolerate this immersion almost indefinitely.
Am I imagining this or did I remember it correctly? Perhaps an MSR literate person can verify that leaving the pump in the bottle is OK.
I have had to tighten the on/off valve after smelling leaking fuel in my pack, however. No big deal because I kept the stove in a plastic bag and the fuel did not escape the plastic. Fuel evaporates quickly anyway so I'm not too concerned by a leak now and then.